Maassen's magnum opus, Der Primat des Bischofs von Rom und die alten Patriarchalkirchen (Bonn, 1853), dealt with two important questions: whether the Roman primacy had existed in the first centuries, and whether the much-discussed sixth canon of the First Council of Nicaea bears witness to the primacy. This work won immediate recognition among scholars, and Count Thun invited him to Pesth in 1855 as professor extraordinarius of Roman Law. Several months later, he was given a professorship of Roman and canon law at Innsbruck, one at Graz in 1860, and one in 1871 at Vienna, where, until he retired in 1894, he attracted many pupils.

In 1873 he became a member of the Vienna Academy of Sciences, in 1885 a life member of the Upper House, and from 1882 till 1897 was a member of the Supreme Court of the Empire. During the Vatican Council he adhered to Döllinger, but was in no real sense an Old Catholic, and in 1882 explicitly retracted all his utterances in favour of that sect. Incited by Savigny's important work on the history of Roman law in the Middle Ages, Maassen began a history of canon law on the same lines. But of this work, which was to have numbered five volumes, he published only the first, "Geschichte der Quellen und der Literatur des kanonischen Rechts im Abendlande bis zum Ausgang des Mittelalters" (Graz, 1870). Several of his articles in the Report (Sitzungsberichte) of the Vienna Academy were practically complements of this work. His "Neun Kapitel über freie Kirche und Fewissenfreiheit" (Graz, 1876) is written in a vehement style; a sweeping condemnation of the PrussianKulturkampf. An amplification of the first chapter appeared under the title: "Ueber die Gründe des Kampfes zwischen dem heidnischen Staate und dem Christentum" (Vienna, 1882). In many respects his "Pseudoisidorstudien" (Vienna, 1885) is a continuation of his masterpiece. He also edited in masterly style one volume of the great "Monumenta Germaniæ Historica: Leges", III (Hanover, 1893), being the "Concilia ævi Merovingensis". Noteworthy, also, is his "Zwei Synoden unter Childeric II" (Graz, 1867). Maassen was often perceived as an aggressive political tactician. He was an adherent of the so-called Federalismus, and strove energetically for the formation of a Catholic Conservative party in Styria, where he belonged for a time to the Diet.